AMBiCon

Aims of the project

Making biological phenomena predictable and to simulate entire cellular systems in the computer would be beneficial for biotechnological production of medication and personalized medicine. The genome-scale development of holistic, detailed, and reliable computer models incorporating physico-chemical constraints can only be feasible by using precise automated methods. This project aims to extend approaches for model creation. The effectiveness of the method are being experimentally validated on large-scale metabolic data. To this end, the project "automated multi-level modeling of biological systems considering physico-chemical constraints" (AMBiCon) has been established as an international collaboration project between the University of California, San Diego, and the University of Tuebingen, Tübingen, Germany.

News

Google Summer of Code 2016 (GSoC)

Google often runs a summer program called Google Summer of Code (GSoC), in which Google pays students to work on open-source software. The students work remotely from wherever they live, on projects organized by various groups under the umbrella of a mentoring organization. In the past, our own standards and software project, SBML (the Systems Biology Markup Language), has been selected and had 3 GSoC slots filled. Google is running GSoC again this year. We have many project ideas involving SBML under the umbrella of the NRNB (National Resource for Network Biology).

NRNB itself has many other possible projects that you could get involved with. Google will select the set of mentoring organizations on Feb. 29. We do not know yet, but we think NRNB stands a good chance of getting into GSoC again this year. Once Google releases the list of organizations, things will heat up quickly and there will not be much time to put together your application, so we are announcing this now, to give students more time to decide and get ready. If you are a student and are interested in the SBML-related projects, you can contact Dr. Andreas Dräger for more information. If you are faculty, perhaps you could suggest this opportunity to some of your students? Additional important details about the GSoC program can be found here.

Important dates (see GSoC2016):

  • 14 March: Student application period opens
  • 25 March: Student application deadline
  • 22 April: Accepted student proposals announced

Vacancies

Tutor for grading exercises and finals in the new lecture “Systems Biology: Simulation of Dynamic Network States”. This assistance job requires some programing experience with one of the languages Mathematica, Maple, MATLAB, R. The position is suitable for students of bioinformatics, biometrics, computer science, mathematics, or physics. For more information see this advertisement: Tutor zur Vorlesung Systems Biology: Simulaiton of Dynamic Network States. The contract will comprise 40 h per month over the full duration of the summer semester 2016.

Open bachelor theses

The following topics are conducted in close collaboration with the Center for Bioinformatics Tuebingen of the University of Tuebingen, Germany:

  • This project is well suitable for students of media informatics, bioinformatics, computer science, and related areas: Animierte biochemische Netzwerke. The aim is the creation of video clips for realistic biochemical networks given new data and manually drawn pathway maps.
  • This project addresses students with interest in programing web applications: Webbasierte Erstellung biochemischer Netzwerke

Open master theses

This topic will be conducted in close collaboration with the Center for Bioinformatics Tuebingen of the University of Tuebingen, Germany: Medikamentenwirkung auf personalisierte Blutmodelle gesunder Probanden. In this project, a new comprehensive model of human blood will be created based on the published models for erythrocytes and platelets. Available data comprise metabolomics of approximately 100 substances within red blood cells, plasma, and platelets as well as SNP profiles of human donors prior and after taking selected drugs. The aim is to draw conclusions on or to predict personalized drug effects.

Publications

  • Michael Römer, Johannes Eichner, Andreas Dräger, Clemens Wrzodek, Finja Wrzodek, and Andreas Zell. ZBIT Bioinformatics Toolbox: a Web-Platform for Systems Biology and Expression Data Analysis. PLoS ONE, February 2016. [ DOI ]
  • Roland Keller, Marcus Klein, Maria Thomas, Andreas Dräger, Ute Metzger, Markus F. Templin, Thomas O. Joos, Wolfgang E. Thasler, Andreas Zell, and Ulrich M. Zanger. Coordinating role of RXRα in downregulating hepatic detoxification during inflammation revealed by fuzzy-logic modeling. PLoS Computational Biology, January 2016. [ DOI ]
  • Zachary A. King, Justin S. Lu, Andreas Dräger, Philip C. Miller, Stephen Federowicz, Joshua A Lerman, Ali Ebrahim, Bernhard O. Palsson, and Nathan E. Lewis. BiGG Models: A platform for integrating, standardizing, and sharing genome-scale models. Nucleic Acids Research, October 2015. [ DOI | link | pdf ]
  • Ali Ebrahim, Eivind Almaas, Eugen Bauer, Aarash Bordbar, Anthony P. Burgard, Roger L. Chang, Andreas Dräger, Iman Famili, Adam M. Feist, Ronan M. T. Fleming, Stephen S. Fong, Vassily Hatzimanikatis, Markus J. Herrgard, Allen Holder, Michael Hucka, Daniel Hyduke, Neema Jamshidi, Sang Yup Lee, Nicolas Le Novère, Joshua A. Lerman, Nathan E. Lewis, Ding Ma, Radhakrishnan Mahadevan, Costas Maranas, Harish Nagarajan, Ali Navid, Jens Nielsen, Lars K. Nielsen, Juan Nogales, Alberto Noronha, Csaba Pal, Bernhard O. Palsson, Jason A. Papin, Kiran R. Patil, Nathan D. Price, Jennifer L. Reed, Michael Saunders, Ryan S. Senger, Nikolaus Sonnenschein, Yuekai Sun, and Ines Thiele. Do Genome-scale Models Need Exact Solvers or Clearer Standards? Molecular Systems Biology, 11(10), October 2015. [ DOI | link | pdf ]
  • Andreas Dräger, Daniel C. Zielinski, Roland Keller, Matthias Rall, Johannes Eichner, and Bernhard O. Palsson. SBMLsqueezer 2: Context-sensitive creation of kinetic equations in biochemical networks. BMC Systems Biology, 9(1):1-17, September 2015. [ DOI | link | PDF ]
  • Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, and Darren J. Wilkinson. Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. Journal of Integrative Bioinformatics, 12(2):271, September 2015. [ DOI | link | PDF ]
  • Laurence Yang, Justin Tan, Edward J. O'Brien, Jonathan Monk, Donghyuk Kim, Howard J. Lia, Pep Charusantia, Ali Ebrahim, Colton J. Lloyd, James T. Yurkovich, Bin Du, Andreas Dräger, Alex Thomas, Yuekai Sun, Michael A. Saunders, and Bernhard O. Palsson. A systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data. Proceedings of the National Academy of Sciences, August 2015. [ DOI | PDF | link ]
  • Zachary A. King, Andreas Dräger, Ali Ebrahim, Nikolaus Sonnenschein, Nathan E. Lewis, and Bernhard Ø. Palsson. Escher: A web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS Computational Biology, , 11(8):e1004321, August 2015 [ DOI | link ].
  • Nicolas Rodriguez, Alex Thomas, Leandro Watanabe, Ibrahim Y. Vazirabad, Victor Kofia, Harold F. Gómez, Florian Mittag, Jakob Matthes, Jan Rudolph, Finja Wrzodek, Eugen Netz, Alexander Diamantikos, Johannes Eichner, Roland Keller, Clemens Wrzodek, Sebastian Fröhlich, Nathan E. Lewis, Chris J. Myers, Nicolas Le Novère, Bernhard Ø. Palsson, Michael Hucka, and Andreas Dräger. JSBML 1.0: providing a smorgasbord of options to encode systems biology models. Bioinformatics, June 2015 [DOI | link ].
  • Alexander Dörr, Roland Keller, Andreas Zell, and Andreas Dräger. SBMLsimulator: a Java tool for model simulation and parameter estimation in systems biology. Computational Biology, December 2014. [DOI | link | PDF ]
  • Andreas Dräger and Bernhard Ø. Palsson. Improving collaboration by standardization efforts in systems biology. Frontiers in Bioengineering, 2(61), December 2014. [ DOI | link ]
  • Claudine Chaouiya, Duncan Berenguier, Sarah M. Keating, Aurelien Naldi, Martijn P. van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan Kowal, Benjamin Wicks, Emanuel Gonçalves, Julien Dorier, Michel Page, Pedro T. Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Dennis Thierffry, Nicolas Le Novère, Julio Saez-Rodriguez, and Tomáš Helikar. SBML Qualitative Models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Systems Biology, 7(1):135, December 2013. [ DOI | link | pdf ]
  • Johannes Eichner, Florian Topf, Andreas Dräger, Clemens Wrzodek, Dierk Wanke, and Andreas Zell. TFpredict and SABINE: Sequence-Based Prediction of Structural and Functional Characteristics of Transcription Factors. PLoS ONE, 8(12):e82238, December 2013. [ DOI | link | pdf ]
  • Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn van Iersel, Sarah Keating, Matthias Rall, Michael Wybrow, Henning Hermjakob, Michael Hucka, Douglas B Kell, Wolfgang Müller, Pedro Mendes, Andreas Zell, Claudine Chaouiya, Julio Saez-Rodriguez, Falk Schreiber, Camille Laibe, Andreas Dräger, and Nicolas Le Novère. Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Systems Biology, 7(1):116, November 2013. [ DOI | link | PDF ]
  • Finja Büchel, Sandra Saliger, Andreas Dräger, Stephanie Hoffmann, Clemens Wrzodek, Andreas Zell, and Philipp J. Kahle. Parkinson's disease: dopaminergic nerve cell model is consistent with experimental finding of increased extracellular transport of α-synuclein. BMC Neuroscience, 14(136), November 2013. [ DOI | link | pdf ]
  • Roland Keller, Alexander Dörr, Akito Tabira, Akira Funahashi, Michael J. Ziller, Richard Adams, Nicolas Rodriguez, Nicolas Le Novère, Noriko Hiroi, Hannes Planatscher, Andreas Zell, and Andreas Dräger. The systems biology simulation core algorithm. BMC Systems Biology, 7:55, July 2013. [ DOI | link | pdf ]
  • Andreas Dräger and Hannes Planatscher. Encyclopedia of Systems Biology, chapter Metabolic Networks, pages 1249-1251. Springer-Verlag, New York, August 2013. [ DOI | link ]
  • Andreas Dräger and Hannes Planatscher. Encyclopedia of Systems Biology, chapter Parameter Estimation, Metabolic Network Modeling, pages 1627-1631. Springer-Verlag, New York, August 2013. [ DOI | link ]

Software releases

Teaching

Conference presentations

Acknowledgements

The project AMBiCon is funded by the 7th EU Framework Program for Research and Technological Development in form of a Marie-Curie International Outgoing Fellowship (IOF) awarded to Andreas Dräger (grant number 332020).

Location

Location

417 Powell-Focht Bioengineering Hall

9500 Gilman Drive La Jolla, CA 92093-0412

Contact Us

Contact Us

In Silico Lab:  858-822-1144

Wet Lab:  858-246-1625

FAX:   858-822-3120

Website Concerns: sbrgit@ucsd.edu

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